Contacts of the helix formed by residues 519 - 528 (chain A) in PDB entry 3I5G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485A GLU* 3.2 44.0 - - + +
488A GLN* 3.7 28.0 - - + -
489A GLN* 3.9 12.6 - - + +
492A ASN* 4.1 10.3 - - - +
516A GLY 3.0 9.4 + - - +
517A LEU 3.0 0.6 - - - -
518A ASP* 1.3 88.1 - - + +
520A GLN* 1.3 62.5 + - - +
521A ALA 3.3 2.9 - - - -
522A CYS* 3.6 7.6 + - - +
523A ILE* 3.0 27.8 + - + +
583A HIS* 6.2 3.4 - - + -
585A TYR* 3.9 15.3 - - + +
700A GLU* 3.8 19.1 - - - +
703A ARG* 5.1 2.0 - - - +
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Residues in contact with GLN 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A GLN* 3.1 23.3 + - - +
516A GLY 3.8 1.4 + - - -
517A LEU* 3.1 34.7 + - + +
519A LEU* 1.3 77.0 - - - +
521A ALA* 1.3 57.8 + - - +
523A ILE* 4.2 8.1 - - - +
524A GLU* 2.6 77.0 + - + +
527A GLU* 4.6 9.7 + - - -
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Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A LEU 4.4 3.0 + - - +
518A ASP 5.5 3.8 - - - +
519A LEU 3.3 0.6 - - - -
520A GLN* 1.3 79.5 - - - +
522A CYS* 1.3 57.2 + - - +
524A GLU* 3.8 8.5 - - - +
525A LEU* 2.9 29.3 + - - +
562A ASN* 5.0 7.5 + - - +
563A PRO* 5.9 2.5 - - + -
564A MET* 3.6 24.0 - - + +
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Residues in contact with CYS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A GLU* 3.7 16.2 - - - +
519A LEU* 3.6 9.9 + - - +
520A GLN 3.2 0.6 - - - -
521A ALA* 1.3 75.1 - - - +
523A ILE* 1.3 67.3 + - - +
525A LEU* 3.0 16.2 + - - +
526A ILE* 3.2 22.1 + - - +
564A MET* 3.8 13.7 - - + +
582A LEU* 4.4 11.4 - - - -
583A HIS 3.8 21.5 - - - +
584A HIS* 3.5 37.2 - - - -
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Residues in contact with ILE 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A TYR* 4.2 5.6 - - + -
485A GLU* 3.4 23.8 - - + +
486A ARG* 3.7 39.5 - - + +
489A GLN* 3.7 31.4 - - + +
519A LEU 3.0 17.9 + - - +
520A GLN* 3.1 11.2 + - - +
522A CYS* 1.3 76.9 - - - +
524A GLU* 1.3 56.3 + - - +
526A ILE* 3.0 13.0 + - - +
527A GLU* 3.0 56.4 + - + +
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Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A GLN* 2.6 60.4 + - - +
521A ALA* 3.8 6.8 - - - +
523A ILE* 1.3 68.2 - - - +
525A LEU* 1.3 62.4 + - - +
526A ILE 2.9 6.3 + - - -
527A GLU* 4.3 8.3 - - - +
528A LYS* 2.7 55.1 + - + +
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ALA 2.9 17.5 + - - +
522A CYS* 3.0 8.2 + - - +
524A GLU* 1.3 76.4 - - - +
526A ILE* 1.3 56.8 + - - +
528A LYS* 4.5 7.1 - - - +
531A GLY* 3.7 2.4 - - - -
532A ILE* 3.0 28.3 + - + +
558A HIS* 3.8 37.5 - - + +
562A ASN* 4.3 11.4 - - - +
564A MET* 3.5 26.5 - - + -
565A PHE* 3.7 20.6 - - + +
582A LEU* 3.2 33.7 - - + -
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Residues in contact with ILE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A LEU* 4.3 10.1 - - + -
482A TYR* 3.7 53.2 - - + -
485A GLU* 5.6 1.1 - - + -
522A CYS* 3.5 17.9 - - - +
523A ILE* 3.0 8.0 + - - +
524A GLU 2.9 0.4 - - - -
525A LEU* 1.3 82.4 - - - +
527A GLU* 1.3 59.7 + - - +
528A LYS 3.9 0.4 - - - -
531A GLY 4.2 0.9 - - - -
532A ILE* 3.8 10.5 + - + -
533A LEU* 3.2 48.3 + - + +
534A SER 4.7 0.5 + - - -
582A LEU* 4.1 28.0 - - + -
584A HIS* 4.2 12.1 - - + -
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A TYR* 2.8 36.6 + - + +
486A ARG* 3.9 15.9 + - - -
520A GLN* 4.6 9.0 + - - -
523A ILE* 3.0 34.9 + - + +
524A GLU* 4.3 4.0 - - - +
526A ILE* 1.3 77.6 - - - +
528A LYS* 1.3 65.1 + - + +
529A PRO* 4.0 2.1 - - - +
533A LEU* 5.2 1.1 - - - -
534A SER* 5.5 3.4 - - - -
652A LYS* 4.7 18.7 + - + +
656A ASN* 4.7 2.6 - - - +
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Residues in contact with LYS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A GLU* 2.7 52.2 + - + +
525A LEU* 4.5 5.7 - - - +
526A ILE 3.9 0.2 - - - -
527A GLU* 1.3 81.8 - - + +
529A PRO* 1.3 69.2 + - + +
530A MET* 4.2 4.0 + - - +
531A GLY* 2.6 40.2 + - - +
534A SER* 4.1 4.0 - - - -
558A HIS* 3.3 32.9 + - - -
562A ASN* 5.2 8.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il